Abstract
The investigation of infectious disease outbreaks relies on the analysis of increasingly complex and diverse data, which offer new prospects for gaining insights into disease transmission processes and informing public health policies. However, the potential of such data can only be harnessed using a number of different, complementary approaches and tools, and a unified platform for the analysis of disease outbreaks is still lacking. In this paper, we present the new R package OutbreakTools, which aims to provide a basis for outbreak data management and analysis in R. OutbreakTools is developed by a community of epidemiologists, statisticians, modellers and bioinformaticians, and implements classes and methods for storing, handling and visualizing outbreak data. It includes real and simulated outbreak datasets. Together with a number of tools for infectious disease epidemiology recently made available in R, OutbreakTools contributes to the emergence of a new, free and open-source platform for the analysis of disease outbreaks.
Highlights
Infectious disease outbreak investigation is a complex task in which a variety of data sources can be exploited for attempting to uncover the spatio-temporal dynamics and transmission pathways of a pathogen in a population
Together with a number of tools for infectious disease epidemiology recently made available in R, OutbreakTools contributes to the emergence of a new, free and open-source platform for the analysis of disease outbreaks
While a number of packages for infectious disease epidemiology have recently been developed in the R software (Jombart et al, 2014; Obadia et al, 2012; Stadler and Bonhoeffer, 2013; Cori et al, 2013), basic tools for storing, handling and visualizing outbreak data have so far been lacking
Summary
Infectious disease outbreak investigation is a complex task in which a variety of data sources can be exploited for attempting to uncover the spatio-temporal dynamics and transmission pathways of a pathogen in a population. OutbreakTools is developed by a community of epidemiologists, statisticians, modellers and bioinformaticians, and implements classes and methods for storing, handling and visualizing outbreak data.
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